Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_006748151.1 THITH_RS10455 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000227685.2:WP_006748151.1 Length = 469 Score = 214 bits (546), Expect = 3e-60 Identities = 146/439 (33%), Positives = 214/439 (48%), Gaps = 60/439 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVP--------ANTIGAA 81 +D + H+ TSP R +A R + W + ++ V DHNVP A+ + Sbjct: 28 IDRHLVHEVTSPQAFEGLR-LAGR----KPWRSDSVLAVPDHNVPTEHREAGIADPVSRT 82 Query: 82 EFQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAF 139 + + + R E G+ + GI H + PE+G PGM +V DSHT T+GA GA Sbjct: 83 QVETLERNVG-EFGLKFFPMRDLRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGALGAL 141 Query: 140 ATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRS 199 A G+G +++ V AT W +M + V GE V AKDV+L IIG IG G T + Sbjct: 142 AFGIGTSEVEHVLATQCLWQKKSRSMLVRVDGELRPGVTAKDVVLAIIGTIGTAGGTGYA 201 Query: 200 VEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA-----------RTGR 248 +EF G I S+ V GRMT+CNMA+E GA+ G++ + +T++YVR R Sbjct: 202 IEFGGAAIRSLSVEGRMTVCNMAIEAGARAGMVAVDEKTIEYVRGRPQAPAGELFERAAL 261 Query: 249 EFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVH------------------- 289 +R SD D+++ D + +EPQV+ + V PV Sbjct: 262 SWRELVSDPDARFDRVVVLDAATIEPQVSWGTSPEMVVPVSGRVPDPALEKDPVRAEGMR 321 Query: 290 ------------RVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRF-IVSPAS 336 ++G D+ F+GSCTN R EDL+ AA V+ RR + V+ +V P S Sbjct: 322 KALRYMGLEPGTPIDGIRPDKVFIGSCTNSRIEDLREAAAVVRGRRKADSVQLAMVVPGS 381 Query: 337 REIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDP 396 + +A +G+ F+ AG PGC CL + L PGE +T+NRNF GR G Sbjct: 382 GLVKQQAEAEGLDRVFLDAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQGQ- 440 Query: 397 ASSVYLANPAVVAESAIEG 415 +L +PA+ A +A+ G Sbjct: 441 GGRTHLVSPALAAAAAVAG 459 Lambda K H 0.320 0.137 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 572 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 428 Length of database: 469 Length adjustment: 33 Effective length of query: 395 Effective length of database: 436 Effective search space: 172220 Effective search space used: 172220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory